waldo 0.1

Protein Subcellular Location Information Package

Waldo tells what everyone already knows.

We have a manuscript in preparation. If you use this in a publication, please let us know so we can (to the best of our knowledge), give you the right citation.

Installation

Dependencies

• python

• lxml

• sqlalchemy

• bottle

bottle is only needed if wish to run the web application (i.e., if you only using the local programming API, then you can skip this step).

Under a debian or Ubuntu system, the following commands will install all needed packages:

sudo apt-get install python-lxml
sudo apt-get install python-sqlalchemy
sudo apt-get install python-bottle

Installation

You can run the install.sh file to get everything working:

./install.sh

The individual steps are:

python setup.py install

This is the standard Python installation command. In order to start using waldo, you need to download all the database files and build the index. The utility script update-waldo should accomplish this:

update-waldo --user
update-waldo
update-waldo --datadir /path/to/datadir --database database.sqlite3

There are three variations (shown above):

1. --user (the default for install.sh) installs waldo locally for this user (under $HOME/.local/share/waldo)

2. Without an argument, it installs it system-wide (you need to have write access to /var/lib/waldo

3. You can specify exactly where to store the data.

The datadir is where waldo will store the downloaded information. It defaults to /var/lib/waldo/data. You can also specify where to store the database file (default is /var/lib/waldo/waldo.sqlite3).

Additionally, you can use the --unsafe flag to speed up the indexing, but if you interrupt the process, the database may be broken:

update-waldo --user --unsafe

Running the Webapp

If you have installed waldo as above, you should execute:

python woof/woof.py

Links

• documentation: http://waldo.readthedocs.org/en/latest/

• github: https://github.com/luispedro/waldo